The following applications are incorporated herein by reference in their entirety:
PCT Application No. PCT/US00/25381 filed on Sep. 15, 2000, published as WO 02/12896, entitled xe2x80x9cMethod for Manipulating Moieties in Microfluidic Systemsxe2x80x9d naming as inventors Xiaobo Wang, Lei Wu, Jing Cheng, Weiping Yand and Junquan Xu;
U.S. patent application Ser. No. 09/678,263, filed on Oct. 3, 2000, now U.S. Pat. No. 6,596,143, entitled xe2x80x9cApparatus for Switching and Manipulating Particles and Method of Use Thereofxe2x80x9d and naming as inventors Xiaobo Wang, Weiping Yang, JunQuan Xu, Jing Cheng and Lei Wu, which corresponds to People""s Republic of China Application Number 00129043.6 entitled xe2x80x9cApparatus for Switching and Manipulating Particles and Method of Use Thereof,xe2x80x9d filed Sep. 27, 2000;
U.S. patent application Ser. No. 09/679,024 filed on Oct. 4, 2000, entitled xe2x80x9cApparatus Containing Multiple Active Force Generating Elements and Uses Thereofxe2x80x9d and naming as inventors Xiaobo Wang, Jing Cheng, Lei Wu, JunQuan Xu and Weiping Yang, which corresponds to People""s Republic of China Application Number 00130563.8, filed Sep. 30, 2000;
U.S. patent application Ser. No. 09/636,104 filed Aug. 10, 2000, entitled xe2x80x9cMethods for Manipulating Moieties in Microfluidic Systems;xe2x80x9d
U.S. patent application Ser. No. 09/684,081 filed Aug. 25, 2000, entitled xe2x80x9cMethods and Compositions for Identifying Nucleic Acid Molecules Using Nucleolytic Activities and Hybridization;xe2x80x9d
U.S. patent application Ser. No. 09/686,737 filed Oct. 10, 2000, entitled xe2x80x9cCompositions and Methods for Separation of Moieties on Chipsxe2x80x9d naming as inventors JunQuan Xu, Xiaobo Wang, Jing Cheng, Weiping Yang and Lei Wu that corresponds to People""s Republic of China Application No. 00131649.4, filed Oct. 9, 2000; and
U.S. Provisional Application No. 60/239,299 filed Oct. 10, 2000, entitled xe2x80x9cAn Integrated Biochip System for Sample Preparation and Analysisxe2x80x9d naming as inventors Jing Cheng et al.
The present application concerns micromachined or microfabricated devices known as xe2x80x9cbiochipsxe2x80x9d and more particularly biochips employing magnetic forces and methods of utilizing such biochips for performing chemical, biological and biochemical reactions and assays.
As a novel and emerging technology in life science and biomedical research during last several years, biochip technology can be applied to many areas of biology, biotechnology and biomedicine including point-mutation detection, DNA sequencing, gene expression, drug screening and clinical diagnosis. Biochips refer to miniaturized devices that can be used for performing chemical and biochemical reactions. Biochips are produced using microelectronic and microfabrication techniques as used in semiconductor industry or other similar techniques, and can be used to integrate and shrink the currently discrete chemical or biochemical analytical processes and devices into microchip-based apparatus. Recent scientific literature shows a plethora of uses for these devices.
The reader s attention is drawn to the following articles for an appreciation of the breadth of biochip uses. Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control by Sosnowski, R. G. etal. (Proc. Natl. Acad. Sci., USA, 94:1119-1123 (1997)) and Large-scale identification, mapping and genotyping of single-nucleotide polymorphisms in the human genome by Wang, D. G. et al. (Science, 280: 1077-1082 (1998)) show current biochip use in detection of point mutations. Accurate sequencing by hybridization for DNA diagnostics and individual genomics by Drmanac, S. et al. (Nature Biotechnol. 16: 54-58 (1998)), Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy by Shoemaker, D. D. et al. (Nature Genet., 14:450-456 (1996)), and Accessing genetic information with high density DNA arrays. by Chee, M et al., (Science, 274:610-614 (1996)) show biochip technology used for DNA sequencing. The use of biochip technology to monitor gene expression is shown in Genome-wide expression monitoring in Saccharomyces cerevisiae by Wodicka, L. et al. (Nature Biotechnol. 15:1359-1367 (1997)), Genomics and human diseasexe2x80x94variations on variation. by Brown, P. O. and Hartwell, L. and Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays by Ruan, Y. et al. (The Plant Journal 15:821-833 (1998)). The use of biochips in drug screening is illustrated in Selecting effective antisense reagents on combinatorial oligonucleotide arrays by Milner, N. et al. (Nature Biotechnol., 15:537-541 (1997)), and Drug target validation and identification of secondary drug target effects using DNA microarray by Marton, M. J. et al. (Nature Medicine, 4:1293-1301 (1998)). Examples of clinical diagnostic use of biochips is illustrated in Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays by Cronin, M. T. et al. (Human Mutation, 7:244-255 (1996)), and Polypyrrole DNA chip on a silicon device: Example of hepatitis C virus genotyping by Livache, T. et al. (Anal. Biochem. 255:188-194 (1998)). These references are intended to give a notion of the wide range of biochip uses.
A variety of biochips have biomolecules (for example, oligonucleotides, cDNA and antibodies) immobilized on their surfaces. There are a number of different approaches to make such chips. For example, the light-directed chemical synthesis process developed by Affymetrix (for example, U.S. Pat. Nos. 5,445,934 and 5,856,174) is a method of synthesizing biomolecules on chip surfaces by combining solid-phase photochemical synthesis with photolithographic fabrication techniques. The chemical deposition approach developed by Incyte Pharmaceutical uses pre-synthesized cDNA probe for directed deposition onto chip surfaces (see, for example, U.S. Pat. No. 5,874,554). The contact-print method developed by Stanford University uses high-speed, high-precision robot-arms to move and control liquid-dispense head for directed cDNA deposition and printing onto chip surfaces (see, for example, Schena, M. et al. Science 270:467-70 (1995)). The University of Washington at Seattle developed a single-nucleotide probe synthesis method by using four piezoelectric deposition heads, which are loaded separately with four types of nucleotide molecules to achieve required deposition of nucleotides and simultaneous synthesis on chip surfaces (see for example, Blanchard, A. P. et al. Biosensors and Bioelectronics 11:687-90 (1996)). Hyseq, Inc. has developed passive membrane devices for sequencing genomes (see, for example, U.S. Pat. No. 5,202,231).
There are two basic types of biochips, for example, passive and active. Passive biochips refer to those on which chemical or biochemical reactions are dependent on passive diffusion of sample molecules. In active biochips reactants are actively moved or concentrated by externally applied forces so that reactions are dependant not only on simple diffusion but also on the applied forces. The majority of the available biochips, for example, oligonucleotide-based DNA chips from Affymetrix and cDNA-based biochips from Incyte Pharmaceuticals, belong to the passive type. There are structural similarities between active and passive biochips. Both types of biochips employ of arrays of different immobilized ligands or ligand molecules. By using various markers, detectable markers, detection systems and indicator molecules (for example, fluorescent dye molecules), the reaction between ligands and other molecules can be monitored and quantified. Thus, an array of different ligands immobilized on a biochip allows for the reaction and monitoring of multiple analyte molecules.
Many current passive biochip designs do not take full advantage of microfabrication and microelectronic technologies. Passive biochips cannot be readily used to achieve fully integration and miniaturization of the entire bioanalytical system from the front-end sample preparation to final molecular quantification/detection. In addition, passive biochips have other disadvantages including low analytical sensitivity, a long reaction time, and difficulties associated with control of temperature, pressure, and electrical fields at individual sites (called units) on the chip surfaces as well as difficulties in controlling the local concentrations of molecules.
On the other hand, active biochips allow versatile functions of molecular manipulation, interaction, hybridization reaction and separation (such as PCR and capillary electrophoresis) by external forces through means such as microfluidic manipulation and electrical manipulation of molecules. However, many such biochips cannot be readily used in high throughput applications. The electronic biochips developed by Nanogen can manipulate and control sample biomolecules with electrical field generated by microelectrodes, leading to significant improvement in reaction speed and detection sensitivity over passive biochips (see, for example, U.S. Pat. Nos. 5,605,662, 5,632,957, and 5,849,486). However, to effectively move biomolecules in their suspension/solutions with electrical fields, electrical conductivity of solutions has to be very low. This significantly limits the choice of buffer solutions used for biochemical assays. Many enzymes and other biomolecules are denatured under conditions of low ionic strength and/or serious non-specific binding occurs to chip surfaces.
The present invention provides a new type of active biochips in which magnetic forces are generated by individually addressable (controllable) units arranged in an array. The magnetic forces are used to control and manipulate magnetically-modified molecules and particles and to promote molecular interactions and/or reactions on the surfaces of chips. Magnetic forces have been widely employed in biological, biochemical and biomedical applications. For example, magnetic-activated cell sorting is a common technique based on selectively binding magnetic particles that has been modified with antibodies to specific cell types within a mixture. After binding, the cell-magnetic particle complexes from the cell mixture are selectively removed using a magnet. (See, for example, Miltenyi, S. et al. High gradient magnetic cell-separation with MACS (Cytometry 11:231-236 (1990)). Other examples were given in U.S. Pat. No. 5,439,586 describing a three-dimensional magnetic filter for separating magnetically labeled particles from non-magnetic particles in a flow stream and in U.S. Pat. No. 5,655,665 disclosing a micromachined magnetic particle separator for microfluidic magnetic separations.